UDiTaS(TM) stands for UniDirectional Targeted Sequencing, a novel sequencing method useful for measuring small indels as well as structural rearrangements, like translocations, in a single reaction.
See details of the method in Giannoukos et al. BMC Genomics (2018) 19:212, https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4561-9
UDiTaS has been tested in python 2.7.13 and requires the python packages and tools listed in the file uditas_env.yml
The code requires setting up two environmental variables
BOWTIE2_INDEXES contains the location of the bowtie2 index files, typically hg38.1.bt2, hg38.2.bt2, etc.
GENOMES_2BIT contains the location of the 2bit files for the genomes used in the analysis, eg hg38.2bit
To test the code create a virtual python environment with
conda env create -f uditas_env.yml
then activate using
source activate uditas_env
To install uditas as an executable run
python setup.py install
To test the installation run
pytest
This will process the test data in
data/fig2a
data/fig2b
data/fig2c
These data are a subsample of the data displayed in Fig 2 of the paper.
uditas is the main command to launch the UDiTaS analysis. The required argument is: dir_sample, the path of the directory with the data to be analyzed.
dir_sample should contain the fastq.gz files for R1, R2, I1 and I2. Used in the demultiplexing step.
dir_sample should also contain the analysis sheet sample_info.csv containing the description of all the samples, with their barcodes and guides used. See examples in the folder data
Once the setup has been run, the code can be run as
uditas ./data/fig2a
The full list of options are:
usage: uditas [-h] [-folder_genome_2bit FOLDER_GENOME_2BIT]
[-skip_demultiplexing SKIP_DEMULTIPLEXING]
[-skip_trimming SKIP_TRIMMING]
[-skip_genome_local_alignment SKIP_GENOME_LOCAL_ALIGNMENT]
[-skip_genome_global_alignment SKIP_GENOME_GLOBAL_ALIGNMENT]
[-process_amplicon PROCESS_AMPLICON]
[-skip_amplicon_global_alignment SKIP_AMPLICON_GLOBAL_ALIGNMENT]
[-check_plasmid_insertions CHECK_PLASMID_INSERTIONS]
[-skip_plasmid_alignment SKIP_PLASMID_ALIGNMENT] [-ncpu NCPU]
[-window_size WINDOW_SIZE]
[-default_amplicon_window_around_cut DEFAULT_AMPLICON_WINDOW_AROUND_CUT]
[-min_MAPQ MIN_MAPQ] [-min_AS MIN_AS]
[-process_AMP_seq_run PROCESS_AMP_SEQ_RUN]
dir_sample
Process UDiTaS data
positional arguments:
dir_sample Directory with the sample to be processed
optional arguments:
-h, --help show this help message and exit
-folder_genome_2bit FOLDER_GENOME_2BIT
Folder containing the 2bit file(s) with the reference
genome being used (default: GENOMES_2BIT)
-skip_demultiplexing SKIP_DEMULTIPLEXING
Skip demultiplexing? Options: 0, 1 (skip) (default: 0)
-skip_trimming SKIP_TRIMMING
Skip adapter trimming? Options: 0, 1 (skip) (default:
0)
-skip_genome_local_alignment SKIP_GENOME_LOCAL_ALIGNMENT
Skip genome-wide local alignment? Options: 0 , 1
(skip) (default: 1)
-skip_genome_global_alignment SKIP_GENOME_GLOBAL_ALIGNMENT
Skip genome-wide global alignment? Options: 0 , 1
(skip) (default: 0)
-process_amplicon PROCESS_AMPLICON
Select row number (0-based) of amplicon to process,
set to all to process all amplicons (default: all)
-skip_amplicon_global_alignment SKIP_AMPLICON_GLOBAL_ALIGNMENT
Skip amplicon global alignment? Options: 0, 1 (skip)
(default: 0)
-check_plasmid_insertions CHECK_PLASMID_INSERTIONS
Check for plasmid insertions. Options: 0 (skip), 1
plamid_name and plasmid_sequence required in
sample_info.csv (default: 1)
-skip_plasmid_alignment SKIP_PLASMID_ALIGNMENT
Skip plasmid alignment? Note, just alignment. Counts
still evaluated. Options: 0, 1 (skip) (default: 0)
-ncpu NCPU Number of CPUs to use (default: 4)
-window_size WINDOW_SIZE
Window size around cut sites used to grab UDiTaS reads
(default: 15)
-default_amplicon_window_around_cut DEFAULT_AMPLICON_WINDOW_AROUND_CUT
Window size around cut sites used to create amplicons
(default: 1000)
-min_MAPQ MIN_MAPQ Minimum mapping quality to include a read (default: 5)
-min_AS MIN_AS Minimum alignment score to include a read (default:
-180)
-process_AMP_seq_run PROCESS_AMP_SEQ_RUN
Set to 1 to process an AMP-seq run using GUIDE-seq
adapters (default: 0)